RNA interference (RNAi) is a natural mechanism in which RNA regulates gene expression. When RNA is utilized by the RNAi mechanism, it alters (e.g., represses or silences) the expression of genes that are complementary in sequence to the regulatory RNA (See, e.g., Nakahara and Carthew, (2004) Curr Opin Cell Biol 16, 127-133). Generally, gene repression occurs via degradation of complementary mRNA transcripts, thus preventing protein product synthesis (See, e.g., Carthew (2001) Curr Opin Cell Biol 12, 244-248). A signature feature of the regulatory RNA is that it has a double helix structure. If double stranded RNA (dsRNA) is present, then it is processed into small RNA fragments 21-25 nucleotides in length by a class of RNaseIII enzymes called the Dicer family. These RNA fragments, called siRNAs, are sufficient to substitute for dsRNA in causing mRNA transcript degradation. Thus, siRNAs are thought to be the direct guides that identify mRNA substrates for degradation.
Once siRNAs are formed, they associate into a nuclease complex termed RNA-induced silencing complex (RISC) that recognizes and cleaves mRNAs. Cleavage of mRNA substrate by RISC is endonucleolytic and occurs at a central site in the region homologous to the siRNA.
RNAi has become a new and powerful approach to rational drug design (e.g., to treat diseases that involve aberrant gene expression). However, one significant drawback to RNAi is that its effect on gene expression is rarely completely potent. This limitation, observed widely, is problematic when a cessation of gene expression is desired or required. Thus, there exists a need to improve RNAi efficacy in research, clinical and therapeutic settings (e.g., to improve RNA-based treatments).